PTCD2

protein-coding

pentatricopeptide repeat domain 2, the group of Pentatricopeptide repeat containing

Gene summary

Enables RNA binding activity. Predicted to be involved in mitochondrion organization and regulation of mRNA processing. Predicted to act upstream of or within several processes, including liver development; muscle cell development; and ventricular cardiac muscle tissue morphogenesis. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024754.5

Inheritance

—

ClinVar variants

U:59B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr5:72,320,367-72,368,395

External References & Databases

Ensembl (ENSG00000049883)

Transcript & Mutation Effects

hg38 • Region Span ~48.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PTCD2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 58

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024754.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			56 clinvar	4 clinvar		60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	59	4	0	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024754.5	RefSeq	NP_079030.3	10	MANE Select
ENST00000380639.10	Ensembl	ENSP00000370013.4	10	MANE Select
NM_001284403.2	RefSeq	NP_001271332.1	7	Standard
NM_001284404.2	RefSeq	NP_001271333.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

kidney development
liver development
mRNA processing
mitochondrion organization
muscle fiber development

Molecular Function

RNA binding

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380639
Coding exons: 10
Length: 39859
Individuals with no LoFs: 125677
Homozygous LoFs: 0
Heterozygous LoFs: 71
Defined: 125748
p: 0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.128	196	201	0.975	0.00000968	2543
Missense (PolyPhen)		33	44.557	0.74062		604
Synonymous	-0.750	88	79.5	1.11	0.00000403	733
Loss of Function	0.503	17	19.4	0.877	9.19e-7	260

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00068	0.00067	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00039	0.00038	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00020	0.00020	rare
South Asian	0.00036	0.00036	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in mitochondrial RNA maturation and mitochondrial respiratory chain function. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.695
RVIS EVS: -0.65
RVIS percentile EVS: 16.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.246

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium